Course Objectives: To introduce the objectives, philosophy and methodology of neuronal
modeling and computational neurophysiology. Topics include how to create models of
membrane channels and neurons; how to create networks by connecting neuron models, and how
to run simulations of their activity and behavior. The course instructs students in the use and
syntax of some of the more popular neural modeling software packages. The computational
neuroanatomy component will include up to three modules: one for morphological tracing, one
for morphological analysis, and one for morphological simulations and/or network connectivity.
Creating and simulating neural models reinforces the concepts learned in NEUR 602, by
illustrating how activity patterns are modulated by different types of membrane channels or
different types of neuron connections.

Format: The course meets three hours a week, in a combination of lecture and electronic
laboratory. The first part of each class will consist of a brief lecture on the neuronal component
to be modeled. The lecture for the remaining class will describe how those components are
modeled, including specific syntax and interaction with other neuronal components. Each
student is expected to repeat on their own computers the modeling commands demonstrated by
the instructor.

Textbook:

Required: The Book of GENESIS. Free Internet Edition (2003) Bower and Beeman (free online
pdf), The NEURON Book (2006) Carnevale and Hines

Assignments and Grading:

In class model construction (20%): At the end of the class period a copy of the practice
commands will be turned in to the instructor.

Homework (40%): Homework will consist of using the commands and components to create
novel models or simulations.

Final project (40%): development of a model using one of the software packages presented in
class. The student is required to develop the model, run simulations, and write a report
describing the model and the simulation results. Projects will be presented orally on the last day
of class, or on Tuesday, May 12 (during Final exam period).

Grading policy: A score of 90 or above generally results in a grade of A- or above, 80 or above
corresponds to a B- or above, and 70 or above results in C- or above. The numerical score is
only a guideline, and is not absolute. The final grades may be determined on a curve if this is to
the students favor and justified in the opinion of the instructor.

Policy regarding missed assignments: Homework may be turned in at most one week late, but
there will be an automatic penalty of 10% deducted from the score. If an absence from class is
anticipated, homework may be emailed, faxed, or sent in on-time with another student. Make-up
exams are not allowed, unless the student has written medical documentation for absence from
an exam.

No extra credit will be given.

Honor Code All exams and homework assignments must follow the guidelines of the GMU
Honor Code as described in the GMU catalog. Students may use books,
notes, and other sources in preparing for exams and homework. However, when taking exams, no
books, notes, or student interaction is allowed. Students may work together on homework, but
each student must contribute and copying is not allowed. Students may not work together on projects.

If you are a student with a disability and you need academic accommodations, please see me and
contact the Office of Disability Resources at 703.993.2474. All academic accommodations must
be arranged through that office.

Syllabus Draft

Homework assignments, and readings for last half of the class will be added later